A novel subspecies-specific primer targeting the gyrase B gene for the detection of Pectobacterium carotovorum subsp. brasiliense

Abstract. Joko T, Soffan A, Muhammad Saifur Rohman MS. 2019. A novel subspecies-specific primer targeting the gyrase B gene for the detection of Pectobacterium carotovorum subsp. brasiliense. Biodiversitas 20: 3042-3048. Pectobacterium carotovorum subsp. brasiliense is one of the major causative bac...

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Autores principales:	Tri Joko, ALAN SOFFAN, MUHAMMAD SAIFUR ROHMAN
Formato:	article
Lenguaje:	EN
Publicado:	MBI & UNS Solo 2019
Materias:	gyrase b, polymerase chain reaction, pectobacterium, soft rot, specific primer Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/2411e626334247909449b343157c8faa
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spelling	oai:doaj.org-article:2411e626334247909449b343157c8faa2021-11-21T21:54:57ZA novel subspecies-specific primer targeting the gyrase B gene for the detection of Pectobacterium carotovorum subsp. brasiliense1412-033X2085-472210.13057/biodiv/d201037https://doaj.org/article/2411e626334247909449b343157c8faa2019-09-01T00:00:00Zhttps://smujo.id/biodiv/article/view/4299https://doaj.org/toc/1412-033Xhttps://doaj.org/toc/2085-4722Abstract. Joko T, Soffan A, Muhammad Saifur Rohman MS. 2019. A novel subspecies-specific primer targeting the gyrase B gene for the detection of Pectobacterium carotovorum subsp. brasiliense. Biodiversitas 20: 3042-3048. Pectobacterium carotovorum subsp. brasiliense is one of the major causative bacterial pathogens of the soft rot disease in various crops. It has a high virulence and a wide range of hosts in the tropics and the subtropics. Most often, conventional methods are not able to accurately distinguish P. carotovorum subsp. brasiliense from other subspecies. Thus, this study aimed to design a specific gyrase B gene (gyrB) -based primers for the detection and identification of soft rot pathogen. The specific primers design was based on the alignment using gyrB gene sequence data from P. carotovorum subsp. brasiliense and other data from the GenBank. The primers comprised of F-gyr-Pcb (5’-CAC AGG CAC CGC TGG CTG TT-3’) and R-gyr-Pcb (5’-CGT CGT TCC ACT GCA ATG CCA-3’) with an amplicon of 336 base pairs. The specificity of the primers pair was verified both in silico and in polymerase chain reaction (PCR) assays, where the primers could only detect P. carotovorum subsp. brasiliense. Primers’ sensitivity was determined by qualitative PCR with a detection limit of less than 0.5 ng/µL of genomic DNA. Hence, the proposed detection tool can be beneficial to advance further studies on the ecology and epidemiology of soft rot diseases.Tri JokoALAN SOFFANMUHAMMAD SAIFUR ROHMANMBI & UNS Soloarticlegyrase b, polymerase chain reaction, pectobacterium, soft rot, specific primerBiology (General)QH301-705.5ENBiodiversitas, Vol 20, Iss 10 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	gyrase b, polymerase chain reaction, pectobacterium, soft rot, specific primer Biology (General) QH301-705.5
spellingShingle	gyrase b, polymerase chain reaction, pectobacterium, soft rot, specific primer Biology (General) QH301-705.5 Tri Joko ALAN SOFFAN MUHAMMAD SAIFUR ROHMAN A novel subspecies-specific primer targeting the gyrase B gene for the detection of Pectobacterium carotovorum subsp. brasiliense
description	Abstract. Joko T, Soffan A, Muhammad Saifur Rohman MS. 2019. A novel subspecies-specific primer targeting the gyrase B gene for the detection of Pectobacterium carotovorum subsp. brasiliense. Biodiversitas 20: 3042-3048. Pectobacterium carotovorum subsp. brasiliense is one of the major causative bacterial pathogens of the soft rot disease in various crops. It has a high virulence and a wide range of hosts in the tropics and the subtropics. Most often, conventional methods are not able to accurately distinguish P. carotovorum subsp. brasiliense from other subspecies. Thus, this study aimed to design a specific gyrase B gene (gyrB) -based primers for the detection and identification of soft rot pathogen. The specific primers design was based on the alignment using gyrB gene sequence data from P. carotovorum subsp. brasiliense and other data from the GenBank. The primers comprised of F-gyr-Pcb (5’-CAC AGG CAC CGC TGG CTG TT-3’) and R-gyr-Pcb (5’-CGT CGT TCC ACT GCA ATG CCA-3’) with an amplicon of 336 base pairs. The specificity of the primers pair was verified both in silico and in polymerase chain reaction (PCR) assays, where the primers could only detect P. carotovorum subsp. brasiliense. Primers’ sensitivity was determined by qualitative PCR with a detection limit of less than 0.5 ng/µL of genomic DNA. Hence, the proposed detection tool can be beneficial to advance further studies on the ecology and epidemiology of soft rot diseases.
format	article
author	Tri Joko ALAN SOFFAN MUHAMMAD SAIFUR ROHMAN
author_facet	Tri Joko ALAN SOFFAN MUHAMMAD SAIFUR ROHMAN
author_sort	Tri Joko
title	A novel subspecies-specific primer targeting the gyrase B gene for the detection of Pectobacterium carotovorum subsp. brasiliense
title_short	A novel subspecies-specific primer targeting the gyrase B gene for the detection of Pectobacterium carotovorum subsp. brasiliense
title_full	A novel subspecies-specific primer targeting the gyrase B gene for the detection of Pectobacterium carotovorum subsp. brasiliense
title_fullStr	A novel subspecies-specific primer targeting the gyrase B gene for the detection of Pectobacterium carotovorum subsp. brasiliense
title_full_unstemmed	A novel subspecies-specific primer targeting the gyrase B gene for the detection of Pectobacterium carotovorum subsp. brasiliense
title_sort	novel subspecies-specific primer targeting the gyrase b gene for the detection of pectobacterium carotovorum subsp. brasiliense
publisher	MBI & UNS Solo
publishDate	2019
url	https://doaj.org/article/2411e626334247909449b343157c8faa
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A novel subspecies-specific primer targeting the gyrase B gene for the detection of Pectobacterium carotovorum subsp. brasiliense

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